The secrets we keep
by LozzFrances
Summary: I wrote this as though Gwen was recruited around the same time as the others.  Jack must make a choice, but will events that transpire push his hand?
1. Chapter 1

Disclaimer-: **Torchwood characters aren't mine. Though I will take them out to play occasionally. Any original characters that may be brought in cannot by used in other stories without my permission.**

**Please read and review, first fanfic so please let me know what you think! If anyone would be kind enough to beta my stories, it would be greatly appreciated. **

Jack wanders out from his office, his eyes are still glazed over from the week before, not really taking in the mess strewn around the Hub. The rest of the team had left at the start of the week, fed up with Jack's erratic antics.

How had this happened? He slowly starts to notice what has become of the place where he spends nearly all his time. Old pizza boxes, beer bottles, chip packets, with an assortment of other trash litter the floor of Torchwood. He remembers Gwen and Ianto being the last to leave, walking out telling him he had to "get his head right." That made Jack think "Maybe I should put my team first, instead of this obsession for taking off all over several different galaxies with The Doctor."

For hours Jack traversed the halls, cells and work areas occasionally kicking around empty bottles, lost in his own thoughts. He goes and sits outside the weevil's cell, staring absently through the glass at the creature. When he'd first recruited his team Jack knew there were going to be issues, differences of opinion. That's what he'd wanted though. A team that would question and test his ideas and theories, bringing their own to the table during the course of their investigations. They had known when first meeting Jack that there was something different about him. Ianto especially realised Jack never saw the world as others did. And with Jack's tendency to disappear sometimes for weeks without explanation, there was dissension in the ranks.

After a year of this Owen finally had had enough and asked Jack where he vanishes too.

"I can't say" was Jack's reply when Owen finally had him cornered.

"Really?" Owen narrowed his eyes and glared. "Can't or won't?"

"It's none of your business Owen" Jack started shuffling papers, he wanted desperately not to have this conversation. "Look..."

"And don't say what you do on your own time is none of my or any of our business" Owen said waving a hand in the direction of the work stations, cutting Jack off mid reply.

"You know that's complete crap Jack! You're gone for weeks at a time, no word, nothing! How can you expect us not to question that?"

Owen had hit a nerve, he could see it written on his boss's face.

"I expect, Owen Harper, that _my _team knows that I always do what's best!" Jack's voice had lowered dangerously, he was now standing stock still in front of the team doctor staring him down. "I will tell all of you where I go, if and when I feel it necessary."

After that, the subject of his disappearances hadn't been broached for a long while. Life at Torchwood seemed to progress as normal (as normal as Torchwood could get). With Gwen and Ianto being... Welsh, Owen getting on everyone's nerves with his sarcastic or snide remarks and Tosh sitting at her desk for hours, discovering the ins and outs of new alien technology. Jack had taken to spending most of his time shut away in his office, when they weren't having team meetings or tracking aliens. Owen's questions had put him on edge, that's not an easy feat. How could he explain to them who The Doctor was? When Jack didn't know himself, for sure. His team never asked again where he'd go. And he'd never told them.

Until the day that mysterious blue box showed up in Cardiff.


	2. Chapter 2

He came to an abrupt stop, well 'stop' might not be the right word. Outside it looked like a small meteor had hit and inside The Doctor was brushing himself off, putting his suit at rights and surveying the damage. The control room was now scattered with debris from what had felt like an earthquake. "Not again!" He thought to himself, walking around, ducking in and out between low hanging live wires and bits of circuitry. "This is what I get for not taking the brakes off, I suppose?" His question echoed around the room. He never expected an answer from his Tardis, but still he would often talk to her.

The Doctor picked up his jacket, pulled his sonic screwdriver out of the metal grate, where it had become lodged during the rough ride and unexpected landing. Unfortunately all systems in the Tardis weren't working as they should. Stepping outside, he was pleasantly surprised that he'd crashed onto Earth, even if that meant being slightly bogged. From the field he was standing in, he now recognised the familiar cityscape of Cardiff. He turned back to the Tardis, grateful to see no exterior damage. Due to the splendid nature of the weather, a stroll seemed to be in order.

The Hub now seemed rather empty, with no one else around. Tosh was grateful for the peace though, nobody around to disturb her. Coming back to her desk she found there was a reading on one of the rift monitors. Since it wasn't a totally unfamiliar signature no alarms had been sounded. She'd always wondered what this blip on the monitors was, usually when this reading came up Jack would tell her to disregard it. This time though he wasn't there to give orders, so Tosh thought it was high time to investigate further.

Tosh could swear the shape on the monitor was square. "How can that be? No other alien ships, or junk getting thrown through the rift ever registers the same." This thought had made her remember others times where this, she supposed, box has shown up on Torchwood's radar. After these occurrences Jack always disappeared without a word of warning. Then he would waltz back into the Hub like it was any other day. Owen had confronted him about this, before the team had left in high dudgeon.

Tosh knew it was time for some answers. Hopefully the others would be willing to help her, or at least listen to her theories.

Sitting in a scantly lit bar somewhere in the centre of Cardiff, Owen was tipping back his third scotch of the day. Watching people walking out after the lunch rush, he wished he to had somewhere better to be. Owen knew that 'somewhere better' at this time of day was usually the Hub, down in the autopsy room or out with the rest of the team running after a weevil or some other creature. The time he'd spent away from Torchwood had done wonders for him. But he knew this brief hiatus from work wouldn't last long.


	3. Chapter 3

Ianto was roused from another rather late lie in. For work he usually had to be out of bed at 0530, so that he could get to The Hub before anyone else and prepare for another day. Besides Jack of course. Ianto often wondered how many hours sleep his boss really got, since he never seemed to need the rest.

He rolled over to retrieve his phone from the night stand, surprised to find it's now 10 in the morning. The little computerised piece of gadgetry was the reason for him waking from another restful nights sleep.

"Tosh?" His question still veiled by sleep.

"Ianto, listen there's someone here in The Hub." Tosh whispered through the phone.

"Yes Tosh you're in there" he said rolling over with intentions of ending the call.

"Not me!" Tosh surely wanted to yell at Ianto, but couldn't for fear of being discovered "Someone else. A man, he's wandering around talking to himself. I tired calling Owen first but there was no answer."

"Um,Tosh?" Ianto was going to laugh but it didn't seem appropriate.

"What?"

"You were trained by our fearless, absent leader to use a firearm proficiently, were you not?" He let some of the humour of the situation come through in his voice.

"I... well yes I was." Ianto could hear her embarrassment. He wondered if he should try and make Tosh see the funny side but decided against it. "Put the poor woman out of her misery" he thought. "Tosh, I'm hanging up. I'll be at Torchwood in an hour." With that he ended the call, swung his legs over the side of the bed and headed for the shower.

Rounding a corner near the millennium centre, Jack walks towards the Hub. Pizza in one hand, an unopened bottle of well-aged scotch in the other. "This is what true loneliness feels like, I suppose" he thinks to himself. After a few weeks of having no one around to keep his mind on Torchwood's work, this is what's he'd resorted to. From the corner of his eye he catches sight of a tall young man in a well fitted suit.

"Ianto!" he shouts across the paved expanse near the water tower.

Ianto turns, confused for a moment as to who's addressing him. He then recognises Jack. At least he thinks it's Jack under the rumpled shirt and stubble.

"Sir?"

"Cut that out Yan. For the 100th time it's Jack not 'sir'.

"I thought you'd disappeared again" Ianto says in a rather unhappy tone. "If you've been here all this time, how did you miss Tosh being inside the Hub, with who she made out to be an escaped mental patient?"

"What?" Jack was on edge now, someone was inside the Hub, _his _Hub. Someone not meant to be there. While he'd been processing this Ianto had continued talking.

"... Only she couldn't get through, so Tosh called me."

Jack looks sideways at the man that makes the best industrial strength coffee.

"A man, talking to himself, she said?"

"Yes, she said that he seemed very interested in the rift manipulator."

"Do you still keep a couple of guns under the desk in the visitor centre?"

"Always, sir."

"Great!" Jack wished he hadn't taken his revolver holster of his belt. Ianto digs under the desk and finds what they need.

Taking one of the pistols from Ianto, he looks at his companion, nods to the door, pushes the button under the desk and strides down the hall towards the lift.

Tosh had finally been able to make her way to the weapons room without being seen by the intruder. Behind the light table she loads 2 handguns. "Now all I need is a clear shot" she thinks, looking over the table back into the main work area. Before she can line up a shot Tosh hears the lift stop and the security door and gates swing open. Jack and Ianto bolt inside and take aim at the man, now engrossed in a program on Tosh's computer.

**I'm going to finish this chapter here. Sorry if it's a little abrupt but it makes way for the next chapter. I hope you're all liking the story so far. Please leave a review, letting me know what you think.**


	4. Chapter 4

So sorry for the massive delay in posting the next chapter(s).

Lots has been happening lately, so I haven't had the inclination to write, let alone the time. Still getting some important things on track...Yes I heard that "_Captain Jack IS important!_" I should have chapter 4 finished, edited and posted by October's end, if not chapter 5 as well.


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